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Biology subjects

Nuy, J. K.

Publications and source records attributed to Nuy, J. K..

2 recordsLinked to original sources

Taxonomic and functional diversity of aquatic heterotrophs is sustained by dissolved organic matter chemodiversity

Dissolved organic matter (DOM) is ubiquitous in aquatic ecosystems and fundamental for planetary processes and ecosystem functioning. While the link between microbial community composition and heterotrophic utilization of DOM has been recognized, the full diversity of organic compounds, their bioavailability, degradability and specific influences on the diversity and function of heterotrophs are still not clear. Here we experimentally investigate heterotrophic bacteria in thirty-three freshwater model communities. We identified 34 different heterotrophs growing in ambient lake DOM with taxonomic affiliations matching abundant freshwater bacterioplankton. We further describe 25 different heterotrophs growing in the phycosphere of M. Aeruginosa and 6 heterotrophs growing on the DOM produced by M. Aeruginosa with taxonomic affiliation in accord to phycosphere heterotrophs. In our experiment we observed that heterotrophs that live in the phycosphere remove more dissolved organic carbon than abundant freshwater heterotrophs. Moreover, phycosphere heterotrophs have bigger genomes than abundant lake bacteria. Altogether of the 4224 chemical features that were resolved by LC-MS, only 1229 were seen in all three treatments. None of the common/shared compounds were removed across all the model communities, suggesting contrasting niches of the studied taxa. Altogether our study highlights how each model community, with its unique taxonomic assemblages and organotroph functioning is upkept by the chemodiversity of DOM.

ecology↗

A genomic perspective on genome size distribution across Earth's microbiomes reveals a tendency to gene loss

Our view of genome size in Archaea and Bacteria has remained skewed as the data used to paint its picture has been dominated by genomes of microorganisms that can be cultivated under laboratory settings. However, the continuous effort to catalog the genetic make-up of Earths microbiomes specifically propelled by recent extensive work on uncultivated microorganisms, provides a unique opportunity to revise our perspective on genome size distribution. Capitalizing on a recently released extensive catalog of tens of thousands of metagenome-assembled genomes, we provide a comprehensive overview of genome size distributions. We observe that the known phylogenetic diversity of environmental microorganisms possesses significantly smaller genomes than the collection of laboratory isolated microorganisms. Aquatic microorganisms average 3.1 Mb, host-associated microbial genomes average 3.0 Mb, terrestrial microorganism average 3.7 Mb and isolated microorganisms average 4.3 Mb. While the environment where the microorganisms live can certainly be linked to genome size, in some cases, evolutionary phylogenetic history can be a stronger predictor. Moreover, ecological strategies such as auxotrophies have a direct impact on genome size. To better understand the ecological drivers of genome size, we expand on the known and the overlooked factors that influence genome size in different environments, phylogenetic groups and trophic strategies.

microbiology↗